Examples with VersionInfo org.vcell.util.document.VersionInfo used on opensource projects

Example 26 with VersionInfo

use of org.vcell.util.document.VersionInfo in project vcell by virtualcell.

the class ServerDocumentManager method removeUserFromGroup0.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 5:43:44 PM)
 * @param bioModelInfo cbit.vcell.biomodel.BioModelInfo
 */
private VersionInfo removeUserFromGroup0(User user, VersionInfo versionInfo, VersionableType vType, Hashtable vInfoHash, String userToAdd) throws DataAccessException {
    // 
    // unpublish from database
    // 
    VersionInfo newVersionInfo = dbServer.groupRemoveUser(user, vType, versionInfo.getVersion().getVersionKey(), userToAdd, false);
    // 
    // replace versionInfo in hashTable
    // 
    vInfoHash.remove(versionInfo.getVersion().getVersionKey());
    vInfoHash.put(newVersionInfo.getVersion().getVersionKey(), newVersionInfo);
    return newVersionInfo;
}

Example 27 with VersionInfo

use of org.vcell.util.document.VersionInfo in project vcell by virtualcell.

the class DBTopLevel method getMathModelXML.

/**
 * This method was created in VisualAge.
 * @return cbit.sql.Versionable
 * @param object cbit.sql.Versionable
 * @param name java.lang.String
 * @param bVersion boolean
 * @exception org.vcell.util.DataAccessException The exception description.
 * @exception java.sql.SQLException The exception description.
 * @exception cbit.sql.RecordChangedException The exception description.
 */
String getMathModelXML(User user, KeyValue key, boolean bEnableRetry) throws DataAccessException, java.sql.SQLException, ObjectNotFoundException {
    Object lock = new Object();
    VersionableType versionableType = VersionableType.MathModelMetaData;
    Connection con = conFactory.getConnection(lock);
    DbDriver driver = getDbDriver(versionableType);
    try {
        // 
        // Getting the corresponding VersionInfo will fail if you don't have permission to the object.
        // This is needed because the DbDriver-level services can return objects directly from the
        // cache without checking for permissions first.
        // 
        // This check is placed in DbTopLevel because this is the client API entry point.
        // Child objects (of the requested object) are given permission by reachablity anyway,
        // so if the user is allowed permission to the parent, no further checks are necessary.
        // 
        Vector<VersionInfo> vInfos = getVersionableInfos(user, key, versionableType, true, true, false);
        if (vInfos.size() == 0) {
            throw new ObjectNotFoundException(versionableType.getTypeName() + " not found");
        }
        return driver.getVersionableXML(con, versionableType, key);
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        if (bEnableRetry && isBadConnection(con)) {
            conFactory.failed(con, lock);
            return getMathModelXML(user, key, false);
        } else {
            handle_DataAccessException_SQLException(e);
            // never gets here;
            return null;
        }
    } finally {
        conFactory.release(con, lock);
    }
}

Example 28 with VersionInfo

use of org.vcell.util.document.VersionInfo in project vcell by virtualcell.

the class DBTopLevel method findReferences.

/**
 * Insert the method's description here.
 * Creation date: (11/6/2005 10:16:41 AM)
 * @return cbit.vcell.modeldb.ReferenceQueryResult
 * @param user cbit.vcell.server.User
 * @param rqs cbit.vcell.modeldb.ReferenceQuerySpec
 */
ReferenceQueryResult findReferences(User user, ReferenceQuerySpec rqs2, boolean bEnableRetry) throws DataAccessException, java.sql.SQLException {
    Object lock = new Object();
    Connection con = conFactory.getConnection(lock);
    try {
        // Use MathDescription for search if ExternalData
        VersionableType rqsVType = null;
        KeyValue[] vTypeKeys = null;
        if (rqs2.isVersionableType()) {
            rqsVType = rqs2.getVersionableType();
            vTypeKeys = new KeyValue[] { rqs2.getKeyValue() };
        } else if (rqs2.isExternalDataIdentiferType()) {
            DbDriver.cleanupDeletedReferences(con, user, rqs2.getExternalDataIdentifier(), false);
            con.commit();
            rqsVType = VersionableType.MathDescription;
            vTypeKeys = getMathDescKeysForExternalData(rqs2.getKeyValue(), user, true);
            if (vTypeKeys == null || vTypeKeys.length == 0) {
                return null;
            }
        }
        if (rqsVType == null) {
            throw new DataAccessException("findAllReferences error: Couldn't determine Query type");
        }
        VersionableFamily finalVersionalbeFamily = null;
        for (int k = 0; k < vTypeKeys.length; k += 1) {
            // Find references
            VersionableFamily vf = getAllReferences(user, vTypeKeys[k], rqsVType, true);
            // Check permission
            if (vf.bDependants()) {
                VersionableTypeVersion[] vtvArr = vf.getUniqueDependants();
                for (int i = 0; i < vtvArr.length; i += 1) {
                    if (vtvArr[i].getVType().equals(VersionableType.BioModelMetaData)) {
                        Vector<VersionInfo> checkedVInfos = getVersionableInfos(user, vtvArr[i].getVersion().getVersionKey(), VersionableType.BioModelMetaData, false, true, true);
                        if (checkedVInfos == null || checkedVInfos.size() == 0) {
                            throw new DataAccessException("References Not Accessible");
                        }
                    } else if (vtvArr[i].getVType().equals(VersionableType.MathModelMetaData)) {
                        Vector<VersionInfo> checkedVInfos = getVersionableInfos(user, vtvArr[i].getVersion().getVersionKey(), VersionableType.MathModelMetaData, false, true, true);
                        if (checkedVInfos == null || checkedVInfos.size() == 0) {
                            throw new DataAccessException("References Not Accessible");
                        }
                    }
                }
            }
            if (finalVersionalbeFamily == null) {
                finalVersionalbeFamily = vf;
            } else {
                VersionableRelationship[] versRelArr = vf.getDependantRelationships();
                for (int r = 0; r < versRelArr.length; r += 1) {
                    finalVersionalbeFamily.addDependantRelationship(versRelArr[r]);
                }
            }
        }
        return new ReferenceQueryResult(finalVersionalbeFamily);
    } catch (Throwable e) {
        lg.error(e.getMessage(), e);
        if (bEnableRetry && isBadConnection(con)) {
            conFactory.failed(con, lock);
            return findReferences(user, rqs2, false);
        } else {
            handle_DataAccessException_SQLException(e);
            // never gets here;
            return null;
        }
    } finally {
        conFactory.release(con, lock);
    }
}